Gene Targeted | Variance Targeted1-a | Cell Type Targeted | Genotype of Cell | Allele-Selectivity1-b |
---|---|---|---|---|
RPA 70 | 1674 T/C | Mia Paca | C | C > T |
HeLa | T | T > C | ||
SW480 | T | T > C | ||
A549 | T | T > C | ||
SW620 | T | T > C | ||
Panc-1 | T | T > C | ||
Replication protein A, 32 kD1-c | 40 G/A | Mia Paca II | G | G > A |
SW480 | G | G = A | ||
Ribonucleotide reductase | 2410A/G | Mia Paca II | G | G > A |
HeLa | A | A > G | ||
2419A/G | Mia Paca II | A | A > G | |
Thymidylate synthase | 1140C/T | Mia Paca II | C | C > T |
SW480 | C | C > T | ||
A549 | C | C > T | ||
RNA polymerase II | 1847C/T | SW480 | C | C > T |
3059C/T | Mia Paca II | T | T > C | |
SW480 | C | C > T | ||
6466T/C | Mia Paca II | C | C > T | |
TATA associated factor 2H | 554G/A | Mia Paca II | G | G > A |
SW480 | G | G > A | ||
A549 | G | G > A | ||
Ribosomal protein S14 | 183G/A | SW480 | G | G > A |
Eukaryotic initiation factor 5A | 623A/G | Mia Paca II | A | G > A |
SW480 | G | G > A | ||
A549 | A | G > A | ||
T24 | G | G > A | ||
MCF7 | A | G > A | ||
SKRC39 | A | G > A | ||
1012C/T | Mia Paca II | C | C > T | |
SW480 | T | T > C | ||
T24 | T | T > C | ||
Alanyl tRNA synthetase | 1013T/C | Mia Paca II | C | C > T |
SW480 | T | T > C | ||
Cysteinyl tRNA synthetase | 1739C/T | T24 | C | C > T |
Glutamyl Prolyl tRNA synthetase | 3247A/G | Mia Paca II | G | G > A |
A549 | G | G > A | ||
MCF7 | A | A > G | ||
4459G/A | A549 | A | A > G | |
Threonyl tRNA synthetase | 1608G/A | Mia Paca II | G | G > A |
1755G/A | T24 | G | G > A | |
2395T/C | SW480 | T | T > C | |
NaK ATPase, alpha-1 subunit | 2538T/C | Mia Paca II | T | T = C |
A549 | T | T = C | ||
T24 | T | T = C | ||
3375G/A | T24 | G | G > A | |
Transferrin receptor | 2387G/A | SW480 | G | G = A |
Sixteen genes were targeted for mRNA suppression. Each variance with a heterozygosity frequency above 20% (a total of 35) was targeted with oligonucleotide complementary to either allele of the variance. The effect of antisense oligonucleotides on mRNA levels was assessed by blotting. Listed in the table are variances successfully targeted by antisense oligonucleotides and the tumor cell lines in which mRNA suppression was observed. Of the 22 sites successfully targeted, 19 showed oligonucleotide-selective mRNA suppression that correlated perfectly with the genotype of each cell type. Genotyping of each cell line for each variance identified only two heterozygous lines, presumably due to frequent LOH in tumor lines. Data from these lines were excluded because of the difficulty of interpretation without knowledge of the ploidy of each allele.
↵1-a Variances at which antisense oligonucleotides suppressed mRNA levels. The number and nucleotide listed refer to the position and variance identified for each cDNA, respectively. Position corresponds to numbering available from Genbank for each cDNA. The most abundant variance is listed first. Accession numbers for each gene are available on request.
↵1-b C>T indicates that the oligonucleotide matched to the “C” allele suppressed target mRNA better than the oligonucleotide matched to the “T” allele, etc.
↵1-c Note that RPA, 32 kDa subunit, was scored as showing oligonucleotide-selective mRNA suppression even though only one of the two cell lines in the table showed differential suppression.